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Altered representation of the spatial code for odors after olfactory classical conditioning; memory trace formation by synaptic recruitment.
Yu D, Ponomarev A, Davis RL. Yu D, et al. Neuron. 2004 May 13;42(3):437-49. doi: 10.1016/s0896-6273(04)00217-x. Neuron. 2004. PMID: 15134640
The rapid recruitment by conditioning of new synapses into the representation of sensory information may be a general mechanism underlying many forms of short-term memory....
The rapid recruitment by conditioning of new synapses into the representation of sensory information may be a general mechanism under …
An adjustable-threshold algorithm for the identification of objects in three-dimensional images.
Ponomarev AL, Davis RL. Ponomarev AL, et al. Bioinformatics. 2003 Jul 22;19(11):1431-5. doi: 10.1093/bioinformatics/btg176. Bioinformatics. 2003. PMID: 12874057
MOTIVATION: To develop a highly accurate, practical and fast automated segmentation algorithm for three-dimensional images containing biological objects. ...RESULTS: A new adjustable-threshold algorithm was developed to efficiently segment fluorescently labeled obje …
MOTIVATION: To develop a highly accurate, practical and fast automated segmentation algorithm for three-dimensional images containing …
Polymer chromosome models and Monte Carlo simulations of radiation breaking DNA.
Ponomarev AL, Sachs RK. Ponomarev AL, et al. Bioinformatics. 1999 Dec;15(12):957-64. doi: 10.1093/bioinformatics/15.12.957. Bioinformatics. 1999. PMID: 10745984
METHODS: Polymer physics and Monte Carlo numerical methods are used to develop a coarse-grained computational approach. Chromatin is modeled as a random walk on a cubic lattice, and the radiation tracks hitting the chromatin are modeled as straight lines hitt …
METHODS: Polymer physics and Monte Carlo numerical methods are used to develop a coarse-grained computational approach. Chromatin is …
Image-based modeling reveals dynamic redistribution of DNA damage into nuclear sub-domains.
Costes SV, Ponomarev A, Chen JL, Nguyen D, Cucinotta FA, Barcellos-Hoff MH. Costes SV, et al. PLoS Comput Biol. 2007 Aug;3(8):e155. doi: 10.1371/journal.pcbi.0030155. PLoS Comput Biol. 2007. PMID: 17676951 Free PMC article.
We used this probability in Monte Carlo simulations to predict DSB locations in synthetic nuclei geometrically described by a complete set of human chromosomes, taking into account microscope optics from real experiments. ...
We used this probability in Monte Carlo simulations to predict DSB locations in synthetic nuclei geometrically described by a complet …
Radiation breakage of DNA: a model based on random-walk chromatin structure.
Ponomarev AL, Sachs RK. Ponomarev AL, et al. J Math Biol. 2001 Oct;43(4):356-76. doi: 10.1007/s002850100098. J Math Biol. 2001. PMID: 12120873
The software models coarse-grained configurations of chromatin and radiation tracks, small-scale details being suppressed in order to obtain statistical results for larger scales, up to the size of a whole chromosome. We here give an analytic counterpart of the numerical m …
The software models coarse-grained configurations of chromatin and radiation tracks, small-scale details being suppressed in order to obtain …
Monte Carlo predictions of DNA fragment-size distributions for large sizes after HZE particle irradiation.
Ponomarev AL, Cucinotta FA, Sachs RK, Brenner DJ. Ponomarev AL, et al. Phys Med. 2001;17 Suppl 1:153-6. Phys Med. 2001. PMID: 11771543
DSB clustering at large scales, from >100 Mbp down to approximately 2 kbp, is modeled using a Monte-Carlo algorithm. A random-walk model of chromatin is combined with a track model, that predicts the radial distribution of energy from an ion, and the RLC ( …
DSB clustering at large scales, from >100 Mbp down to approximately 2 kbp, is modeled using a Monte-Carlo algorithm. A rand …
A polymer, random walk model for the size-distribution of large DNA fragments after high linear energy transfer radiation.
Ponomarev AL, Brenner D, Hlatky LR, Sachs RK. Ponomarev AL, et al. Radiat Environ Biophys. 2000 Jun;39(2):111-20. doi: 10.1007/s004119900040. Radiat Environ Biophys. 2000. PMID: 10929379
A random-walk, coarse-grained polymer model for chromatin is combined with a simple track structure model in Monte Carlo software called DNAbreak and is applied to data on alpha-particle irradiation of V-79 cells. ...Fragment-size distributions obtained using DNAbre
A random-walk, coarse-grained polymer model for chromatin is combined with a simple track structure model in Monte Carlo softw
Locations of radiation-produced DNA double strand breaks along chromosomes: a stochastic cluster process formalism.
Sachs RK, Ponomarev AL, Hahnfeldt P, Hlatky LR. Sachs RK, et al. Math Biosci. 1999 Jul;159(2):165-87. doi: 10.1016/s0025-5564(99)00019-x. Math Biosci. 1999. PMID: 10414032
We therefore model DSB positions along a chromosome as a stationary Poisson cluster process, i.e. a stochastic process consisting of secondary point processes whose locations are determined by a primary point process that is Poisson. Each secondary pro …
We therefore model DSB positions along a chromosome as a stationary Poisson cluster process, i.e. a stochastic process …
Subtraction of background damage in PFGE experiments on DNA fragment-size distributions.
Ponomarev AL, Belli M, Hahnfeldt PJ, Hlatky L, Sachs RK, Cucinotta FA. Ponomarev AL, et al. Radiat Environ Biophys. 2007 Jun;46(2):155-60. doi: 10.1007/s00411-007-0098-z. Epub 2007 Apr 4. Radiat Environ Biophys. 2007. PMID: 17406880
The non-random distribution of DNA breakage in pulsed-field gel electrophoresis (PFGE) experiments poses a problem of proper subtraction of the background damage to obtain a fragment-size distribution due to radiation only. ...Previously a new generalized for …
The non-random distribution of DNA breakage in pulsed-field gel electrophoresis (PFGE) experiments poses a problem of proper subtract …
Chromatin loops are responsible for higher counts of small DNA fragments induced by high-LET radiation, while chromosomal domains do not affect the fragment sizes.
Ponomarev AL, Cucinotta FA. Ponomarev AL, et al. Int J Radiat Biol. 2006 Apr;82(4):293-305. doi: 10.1080/09553000600637716. Int J Radiat Biol. 2006. PMID: 16690597
MATERIALS AND METHODS: The yields of DSB (double-strand breaks) induced by high-LET radiation were calculated using a track structure model along with a polymer model of DNA packed in the cell nucleus. ...Calculations were carried out for a range of particles …
MATERIALS AND METHODS: The yields of DSB (double-strand breaks) induced by high-LET radiation were calculated using a track structure …
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